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- PDB-3bap: Crystal Structure of the 25 kDa Subunit of Human Cleavage Factor Im -

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Basic information

Entry
Database: PDB / ID: 3bap
TitleCrystal Structure of the 25 kDa Subunit of Human Cleavage Factor Im
ComponentsCleavage and polyadenylation specificity factor subunit 5
KeywordsRNA BINDING PROTEIN / CPSF5 / RNA processing / cleavage factor / mRNA processing / Nucleus / Phosphoprotein / RNA-binding
Function / homology
Function and homology information


positive regulation of pro-B cell differentiation / : / mRNA cleavage factor complex / Processing of Intronless Pre-mRNAs / positive regulation of stem cell differentiation / mRNA cleavage and polyadenylation specificity factor complex / mRNA alternative polyadenylation / mRNA 3'-UTR AU-rich region binding / paraspeckles / mRNA 3'-end processing ...positive regulation of pro-B cell differentiation / : / mRNA cleavage factor complex / Processing of Intronless Pre-mRNAs / positive regulation of stem cell differentiation / mRNA cleavage and polyadenylation specificity factor complex / mRNA alternative polyadenylation / mRNA 3'-UTR AU-rich region binding / paraspeckles / mRNA 3'-end processing / mRNA 3'-end processing / protein heterotetramerization / RNA Polymerase II Transcription Termination / post-transcriptional regulation of gene expression / : / Processing of Capped Intron-Containing Pre-mRNA / centriolar satellite / protein tetramerization / mRNA processing / histone deacetylase binding / cell differentiation / nuclear body / mRNA binding / centrosome / chromatin binding / protein homodimerization activity / RNA binding / nucleoplasm / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Cleavage/polyadenylation specificity factor subunit 5 / Nucleotide hydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Cleavage and polyadenylation specificity factor subunit 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.85 Å
AuthorsCoseno, M. / Doublie, S.
CitationJournal: Nucleic Acids Res. / Year: 2008
Title: Crystal structure of the 25 kDa subunit of human cleavage factor Im.
Authors: Coseno, M. / Martin, G. / Berger, C. / Gilmartin, G. / Keller, W. / Doublie, S.
History
DepositionNov 8, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cleavage and polyadenylation specificity factor subunit 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5392
Polymers26,4471
Non-polymers921
Water3,027168
1
A: Cleavage and polyadenylation specificity factor subunit 5
hetero molecules

A: Cleavage and polyadenylation specificity factor subunit 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0784
Polymers52,8942
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area2800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.115, 80.115, 72.209
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Cleavage and polyadenylation specificity factor subunit 5 / / Cleavage and polyadenylation specificity factor 25 kDa subunit / CPSF 25 kDa subunit / Pre-mRNA ...Cleavage and polyadenylation specificity factor 25 kDa subunit / CPSF 25 kDa subunit / Pre-mRNA cleavage factor Im 25 kDa subunit / Nucleoside diphosphate-linked moiety X motif 21 / Nudix motif 21


Mass: 26446.824 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NUDT21, CFIM25, CPSF25, CPSF5 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) pLysS / References: UniProt: O43809
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 168 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.37 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 25% PEG 3350, 0.2M Magnesium chloride, 0.1M Tris-HCl pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97923, 0.97939, 0.97166
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 3, 2006 / Details: mirrors
RadiationMonochromator: DCM - PAIR OF FLAT SI CRYSTALS / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979231
20.979391
30.971661
ReflectionRedundancy: 6.6 % / Av σ(I) over netI: 14.2 / Number: 148933 / Rmerge(I) obs: 0.073 / Χ2: 1.05 / D res high: 1.85 Å / D res low: 30 Å / Num. obs: 22468 / % possible obs: 96.5
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
3.983097.810.0461.0736.6
3.163.9899.410.0631.0326.9
2.763.1699.410.0891.0717
2.512.7699.610.1161.0596.9
2.332.5199.910.1581.0157
2.192.3310010.2221.0166.9
2.082.1999.510.2831.0476.8
1.992.0897.510.351.066.4
1.921.999110.4491.0616.4
1.851.9280.610.5771.0635.2
ReflectionResolution: 1.82→30 Å / Num. all: 23255 / Num. obs: 22805 / % possible obs: 98.1 % / Redundancy: 6.8 % / Biso Wilson estimate: 31.752 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 16.09
Reflection shellResolution: 1.82→1.89 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.0517 / Mean I/σ(I) obs: 2.2

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT3.004data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementResolution: 1.85→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflection
Rfree0.244 2265 9.7 %
Rwork0.226 --
obs0.226 22805 98.1 %
Solvent computationBsol: 38.14 Å2
Displacement parametersBiso mean: 38.783 Å2
Baniso -1Baniso -2Baniso -3
1-2.913 Å2-1.67 Å20 Å2
2--2.913 Å20 Å2
3----5.826 Å2
Refinement stepCycle: LAST / Resolution: 1.85→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1643 0 6 168 1817
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d1.339
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.4891.5
X-RAY DIFFRACTIONc_mcangle_it2.3212
X-RAY DIFFRACTIONc_scbond_it2.1622
X-RAY DIFFRACTIONc_scangle_it3.3682.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramCNS_TOPPAR:protein.top
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.paramCNS_TOPPAR:dna-rna.top
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top
X-RAY DIFFRACTION4CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top

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